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Advances in Targeting Canonical and Non-canonical Nucleic Acids Structures

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A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Medicinal Chemistry".

Deadline for manuscript submissions: closed (30 June 2022) | Viewed by 11949

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Special Issue Editors

Dr. Angelo Spinello

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Guest Editor

CNR-IOM Democritos and International School for Advanced Studies (SISSA), Trieste, Italy
Interests: molecular modeling; computer-aided drug design; molecular dynamics; QM/MM; anticancer drugs

Prof. Dr. Giampaolo Barone

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Guest Editor

Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Viale delle Scienze, Edificio 17, 90128 Palermo, Italy
Interests: bioinorganic chemistry; computational chemistry; electron spectroscopy; host-guest binding; transition metal chemistry

Dr. Antonio Monari

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Guest Editor

Theoretical Physics and Theoretical Chemistry Laboratory (LPCT), University of Lorraine and CNRS, Nancy, France
Interests: molecular modeling and simulation; theoretical photophysics and photochemistry; time resolved spectroscopy; non-adiabatic phenomena; structural biophysics; DNA photosensitization; DNA lesions and repair mechanism; epigenetic regulations
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Special Issue Information

Dear Colleagues,

The maintenance of the nucleic acid structure is essential to assure the correct realization of their biological function. This includes duplication, transduction, the fine regulation of gene expression, and epigenetics. Hence, important studies dealing with the structure of isolated nucleic acids in different environments or of DNA interacting with proteins are actively performed and have allowed considerable advancements and the recognition of fine regulatory mechanisms, such as the role played by chromatin compaction in epigenetic regulations.

In addition, it is presently well recognized that under physiological conditions and in cellular environments, particular nucleic acid sequences can fold into biologically relevant “noncanonical” topologies. These peculiar structures can involve up to four nucleic acid strands, including, among others, hairpins, triplexes, G-quadruplexes, and i-motifs. Interestingly, these nucleic acid sequences are typically located within regions of the genome related to critical biological processes, such as gene regulatory sequences or telomeres, often involved in a number of human diseases, making them attractive molecular targets for drug design. Therefore, understanding the mechanistic details behind the stabilization of peculiar nucleic acid structural motifs, also due to their interaction with proteins and driving the formation of noncanonical conformations, along with their stabilization using small molecules/metal complexes, are of pivotal importance for future biomedical applications. In this regard, molecular modeling techniques (e.g., docking, extended molecular dynamics simulations, enhanced sampling methods, QM/MM calculations) are increasingly used to assist and partially rationalize experimental studies, providing the possibility to describe at the atomistic level the molecular recognition process and the structural evolution, including allosteric modulation, or to simulate important photophysical properties.

In this Special Issue, we invite the submission of short communications, original research articles, and reviews focusing on the biophysical determination and regulation of canonical and noncanonical nucleic acid/protein complexes, including, among others, histones or histon-like proteins, transcription factors, and repair and duplication enzymes. The interaction of small molecules/metal complexes with canonical/noncanonical nucleic acid structures, as well as the effect of DNA lesions on the molecular structure, will also constitute a particular focus of this issue. Moreover, research contributions combining molecular modeling along with experimental structural, photophysical, and molecular biology techniques (e.g., Cryo-EM, X-ray, UV-Vis spectroscopy, circular dichroism, FRET, fluorescence analyses, etc.) able to sinergically shed light into the drug/target binding mechanism are particularly welcomed.

Dr. Angelo Spinello
Dr. Antonio Monari
Prof. Dr. Giampaolo Barone
Guest Editors

Manuscript Submission Information

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Keywords

Noncanonical DNA/RNA structures
DNA sensitization
Molecular modeling
Molecular recognition
Anticancer drugs
Nucleic acid/protein complexes

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Published Papers (4 papers)

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Research

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13 pages, 4859 KiB

Open AccessArticle

High-Energy Long-Lived Emitting Mixed Excitons in Homopolymeric Adenine-Thymine DNA Duplexes

by Ignacio Vayá, Thomas Gustavsson and Dimitra Markovitsi

Molecules 2022, 27(11), 3558; https://doi.org/10.3390/molecules27113558 - 31 May 2022

Cited by 2 | Viewed by 1795

Abstract

The publication deals with polymeric pA●pT and oligomeric A₂₀●T₂₀ DNA duplexes whose fluorescence is studied by time-correlated single photon counting. It is shown that their emission on the nanosecond timescale is largely dominated by high-energy components peaking at a wavelength shorter than 305 nm. Because of their anisotropy (0.02) and their sensitivity to base stacking, modulated by the duplex size and the ionic strength of the solution, these components are attributed to mixed ππ*/charge transfer excitons. As high-energy long-lived excited states may be responsible for photochemical reactions, their identification via theoretical studies is an important challenge. Full article

(This article belongs to the Special Issue Advances in Targeting Canonical and Non-canonical Nucleic Acids Structures)

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14 pages, 2097 KiB

Open AccessArticle

Biophysical Characterization of Novel DNA Aptamers against K103N/Y181C Double Mutant HIV-1 Reverse Transcriptase

by Siriluk Ratanabunyong, Supaphorn Seetaha, Supa Hannongbua, Saeko Yanaka, Maho Yagi-Utsumi, Koichi Kato, Atchara Paemanee and Kiattawee Choowongkomon

Molecules 2022, 27(1), 285; https://doi.org/10.3390/molecules27010285 - 3 Jan 2022

Cited by 3 | Viewed by 2450

Abstract

The human immunodeficiency virus type-1 Reverse Transcriptase (HIV-1 RT) plays a pivotal role in essential viral replication and is the main target for antiviral therapy. The anti-HIV-1 RT drugs address resistance-associated mutations. This research focused on isolating the potential specific DNA aptamers against K103N/Y181C double mutant HIV-1 RT. Five DNA aptamers showed low IC50 values against both the KY-mutant HIV-1 RT and wildtype (WT) HIV-1 RT. The kinetic binding affinity forms surface plasmon resonance of both KY-mutant and WT HIV-1 RTs in the range of 0.06–2 μM and 0.15–2 μM, respectively. Among these aptamers, the KY44 aptamer was chosen to study the interaction of HIV-1 RTs-DNA aptamer complex by NMR experiments. The NMR results indicate that the aptamer could interact with both WT and KY-mutant HIV-1 RT at the NNRTI drug binding pocket by inducing a chemical shift at methionine residues. Furthermore, KY44 could inhibit pseudo-HIV particle infection in HEK293 cells with nearly 80% inhibition and showed low cytotoxicity on HEK293 cells. These together indicated that the KY44 aptamer could be a potential inhibitor of both WT and KY-mutant HIV-RT. Full article

(This article belongs to the Special Issue Advances in Targeting Canonical and Non-canonical Nucleic Acids Structures)

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19 pages, 2114 KiB

Open AccessArticle

Electronic Circular Dichroism Spectra of DNA Quadruple Helices Studied by Molecular Dynamics Simulations and Excitonic Calculations including Charge Transfer States

by Haritha Asha, James A. Green, Lara Martinez-Fernandez, Luciana Esposito and Roberto Improta

Molecules 2021, 26(16), 4789; https://doi.org/10.3390/molecules26164789 - 7 Aug 2021

Cited by 4 | Viewed by 2583

Abstract

We here investigate the Electronic Circular Dichroism (ECD) Spectra of two representative Guanine-rich sequences folded in a Quadruple helix (GQ), by using a recently developed fragment diabatisation based excitonic model (FrDEx). FrDEx can include charge transfer (CT) excited states and consider the effect of the surrounding monomers on the local excitations (LEs). When applied to different structures generated by molecular dynamics simulations on a fragment of the human telomeric sequence (Tel21/22), FrDEx provides spectra fully consistent with the experimental one and in good agreement with that provided by quantum mechanical (QM) method used for its parametrization, i.e., TD-M05-2X. We show that the ECD spectrum is moderately sensitive to the conformation adopted by the bases of the loops and more significantly to the thermal fluctuations of the Guanine tetrads. In particular, we show how changes in the overlap of the tetrads modulate the intensity of the ECD signal. We illustrate how this correlates with changes in the character of the excitonic states at the bottom of the

L_{a}

and

L_{b}

bands, with larger LE and CT involvement of bases that are more closely stacked. As an additional test, we utilised FrDEx to compute the ECD spectrum of the monomeric and dimeric forms of a GQ forming sequence T30695 (5

^{'}

TGGGTGGGTGGGTGGG3

^{'}

), i.e., a system containing up to 24 Guanine bases, and demonstrated the satisfactory reproduction of the experimental and QM reference results. This study provides new insights on the effects modulating the ECD spectra of GQs and, more generally, further validates FrDEx as an effective tool to predict and assign the spectra of closely stacked multichromophore systems. Full article

(This article belongs to the Special Issue Advances in Targeting Canonical and Non-canonical Nucleic Acids Structures)

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Review

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53 pages, 21235 KiB

Open AccessReview

New Insights on the Interaction of Phenanthroline Based Ligands and Metal Complexes and Polyoxometalates with Duplex DNA and G-Quadruplexes

by Ángel Sánchez-González, Nuno A. G. Bandeira, Iker Ortiz de Luzuriaga, Frederico F. Martins, Sawssen Elleuchi, Khaled Jarraya, Jose Lanuza, Xabier Lopez, Maria José Calhorda and Adrià Gil

Molecules 2021, 26(16), 4737; https://doi.org/10.3390/molecules26164737 - 5 Aug 2021

Cited by 25 | Viewed by 3968

Abstract

This work provides new insights from our team regarding advances in targeting canonical and non-canonical nucleic acid structures. This modality of medical treatment is used as a form of molecular medicine specifically against the growth of cancer cells. Nevertheless, because of increasing concerns about bacterial antibiotic resistance, this medical strategy is also being explored in this field. Up to three strategies for the use of DNA as target have been studied in our research lines during the last few years: (1) the intercalation of phenanthroline derivatives with duplex DNA; (2) the interaction of metal complexes containing phenanthroline with G-quadruplexes; and (3) the activity of Mo polyoxometalates and other Mo-oxo species as artificial phosphoesterases to catalyze the hydrolysis of phosphoester bonds in DNA. We demonstrate some promising computational results concerning the favorable interaction of these small molecules with DNA that could correspond to cytotoxic effects against tumoral cells and microorganisms. Therefore, our results open the door for the pharmaceutical and medical applications of the compounds we propose. Full article

(This article belongs to the Special Issue Advances in Targeting Canonical and Non-canonical Nucleic Acids Structures)

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